upgrade myst-parser dep to 1.0

Author: aleivag

.pre-commit-config.yaml

@@ -48,7 +48,7 @@ repos:
       args: [--config-file=pyproject.toml]
       additional_dependencies:
       - importlib_metadata
-      - myst-parser~=0.18.0
+      - myst-parser~=1.0.0
       - "sphinx~=5.0"
       - nbclient
       - types-PyYAML

myst_nb/core/config.py

@@ -130,7 +130,7 @@ def __post_init__(self):
         default_factory=dict,
         metadata={
             "help": "Custom formats for reading notebook; suffix -> reader",
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             "sections": (Section.global_lvl, Section.read),
         },
     )
@@ -184,7 +184,7 @@ def __post_init__(self):
             "validator": deep_mapping(instance_of(str), instance_of(str)),
             "help": "Mapping of kernel name regex to replacement kernel name"
             "(applied before execution)",
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             "sections": (Section.global_lvl, Section.execute),
         },
     )
@@ -220,7 +220,7 @@ def __post_init__(self):
             "validator": deep_iterable(instance_of(str)),
             "help": "Exclude (POSIX) glob patterns for notebooks",
             "legacy_name": "execution_excludepatterns",
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             "sections": (Section.global_lvl, Section.execute),
         },
     )
@@ -387,7 +387,7 @@ def __post_init__(self):
             "help": "Overrides for the base render priority of mime types: "
             "list of (builder name, mime type, priority)",
             # TODO how to allow this in docutils?
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             "sections": (Section.global_lvl, Section.file_lvl, Section.render),
         },
         repr=False,
@@ -454,7 +454,7 @@ def __post_init__(self):
         metadata={
             "validator": deep_mapping(instance_of(str), instance_of((str, int))),
             "help": "Options for image outputs (class|alt|height|width|scale|align)",
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             # TODO backward-compatible change to "image_options"?
             "cell_key": "image",
             "sections": (
@@ -471,7 +471,7 @@ def __post_init__(self):
         metadata={
             "validator": deep_mapping(instance_of(str), instance_of((str, int))),
             "help": "Options for figure outputs (classes|name|caption|caption_before)",
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             "cell_key": "figure",
             "sections": (
                 Section.global_lvl,
@@ -505,7 +505,7 @@ def __post_init__(self):
                 instance_of(str), deep_mapping(instance_of(str), instance_of(str))
             ),
             "help": "Javascript to be loaded on pages containing ipywidgets",
-            "docutils_exclude": True,
+            "omit": ["docutils"],
             "sections": (Section.global_lvl, Section.render),
         },
         repr=False,

myst_nb/core/read.py

@@ -242,7 +242,6 @@ def _flush_markdown(start_line, token, md_metadata):
     md_metadata: dict = {}
 
     for token in tokens:
-
         nesting_level += token.nesting
 
         if nesting_level != 0:
@@ -313,25 +312,22 @@ class _MockDirective:
 
 
 def _read_fenced_cell(token, cell_index, cell_type):
-    from myst_parser.parsers.directives import (
-        DirectiveParsingError,
-        parse_directive_text,
-    )
+    from myst_parser.parsers.directives import parse_directive_text
 
-    try:
-        _, options, body_lines, _ = parse_directive_text(
-            directive_class=_MockDirective,
-            first_line="",
-            content=token.content,
-            validate_options=False,
-        )
-    except DirectiveParsingError as err:
+    result = parse_directive_text(
+        directive_class=_MockDirective,
+        first_line="",
+        content=token.content,
+        validate_options=False,
+    )
+    if result.warnings:
         raise MystMetadataParsingError(
             "{} cell {} at line {} could not be read: {}".format(
-                cell_type, cell_index, token.map[0] + 1, err
+                cell_type, cell_index, token.map[0] + 1, result.warnings[0]
             )
         )
-    return options, body_lines
+
+    return result.options, result.body
 
 
 def _read_cell_metadata(token, cell_index):

myst_nb/core/render.py

@@ -192,7 +192,6 @@ def render_nb_cell_code(self: SelfType, token: SyntaxTreeNode) -> None:
 
         self.add_line_and_source_path(cell_container, token)
         with self.current_node_context(cell_container, append=True):
-
             # render the code source code
             if not remove_input:
                 cell_input = nodes.container(
@@ -311,11 +310,6 @@ class MimeData:
     """Index of the output in the cell"""
     line: int | None = None
     """Source line of the cell"""
-    md_headings: bool = False
-    """Whether to render headings in text/markdown blocks."""
-    # we can only do this if know the content will be rendered into the main body
-    # of the document, e.g. not inside a container node
-    # (otherwise it will break the structure of the AST)
 
     @property
     def string(self) -> str:
@@ -599,9 +593,7 @@ def render_markdown(self, data: MimeData) -> list[nodes.Element]:
         fmt = self.renderer.get_cell_level_config(
             "render_markdown_format", data.cell_metadata, line=data.line
         )
-        return self._render_markdown_base(
-            data, fmt=fmt, inline=False, allow_headings=data.md_headings
-        )
+        return self._render_markdown_base(data, fmt=fmt, inline=False)
 
     def render_text_plain(self, data: MimeData) -> list[nodes.Element]:
         """Render a notebook text/plain mime data output."""
@@ -754,9 +746,7 @@ def render_markdown_inline(self, data: MimeData) -> list[nodes.Element]:
         fmt = self.renderer.get_cell_level_config(
             "render_markdown_format", data.cell_metadata, line=data.line
         )
-        return self._render_markdown_base(
-            data, fmt=fmt, inline=True, allow_headings=data.md_headings
-        )
+        return self._render_markdown_base(data, fmt=fmt, inline=True)
 
     def render_text_plain_inline(self, data: MimeData) -> list[nodes.Element]:
         """Render a notebook text/plain mime data output."""
@@ -797,7 +787,7 @@ def render_widget_view_inline(self, data: MimeData) -> list[nodes.Element]:
         return self.render_widget_view(data)
 
     def _render_markdown_base(
-        self, data: MimeData, *, fmt: str, inline: bool, allow_headings: bool
+        self, data: MimeData, *, fmt: str, inline: bool
     ) -> list[nodes.Element]:
         """Base render for a notebook markdown mime output (block or inline)."""
         psuedo_element = nodes.Element()  # element to hold the parsed markdown
@@ -833,7 +823,6 @@ def _render_markdown_base(
                     data.string,
                     data.line or 0,
                     inline=inline,
-                    allow_headings=allow_headings,
                 )
         finally:
             # restore the parser

myst_nb/docutils_.py

@@ -19,9 +19,6 @@
     create_warning,
     token_line,
 )
-from myst_parser.parsers.docutils_ import (
-    DOCUTILS_EXCLUDED_ARGS as DOCUTILS_EXCLUDED_ARGS_MYST,
-)
 from myst_parser.parsers.docutils_ import Parser as MystParser
 from myst_parser.parsers.docutils_ import create_myst_config, create_myst_settings_spec
 from myst_parser.parsers.mdit import create_md_parser
@@ -81,7 +78,7 @@ class Parser(MystParser):
     settings_spec = (
         "MyST-NB options",
         None,
-        create_myst_settings_spec(DOCUTILS_EXCLUDED_ARGS, NbParserConfig, "nb_"),
+        create_myst_settings_spec(NbParserConfig, "nb_"),
         *MystParser.settings_spec,
     )
     """Runtime settings specification."""
@@ -116,18 +113,14 @@ def _parse(self, inputstring: str, document: nodes.document) -> None:
 
         # get markdown parsing configuration
         try:
-            md_config = create_myst_config(
-                document.settings, DOCUTILS_EXCLUDED_ARGS_MYST
-            )
+            md_config = create_myst_config(document.settings)
         except (TypeError, ValueError) as error:
             logger.error(f"myst configuration invalid: {error.args[0]}")
             md_config = MdParserConfig()
 
         # get notebook rendering configuration
         try:
-            nb_config = create_myst_config(
-                document.settings, DOCUTILS_EXCLUDED_ARGS, NbParserConfig, "nb_"
-            )
+            nb_config = create_myst_config(document.settings, NbParserConfig, "nb_")
         except (TypeError, ValueError) as error:
             logger.error(f"myst-nb configuration invalid: {error.args[0]}")
             nb_config = NbParserConfig()
@@ -301,7 +294,6 @@ def _render_nb_cell_code_outputs(
                 self.add_line_and_source_path_r(_nodes, token)
                 self.current_node.extend(_nodes)
             elif output.output_type in ("display_data", "execute_result"):
-
                 # Note, this is different to the sphinx implementation,
                 # here we directly select a single output, based on the mime_priority,
                 # as opposed to output all mime types, and select in a post-transform

myst_nb/ext/glue/directives.py

@@ -106,7 +106,6 @@ def run(self) -> List[nodes.Node]:
             },
             output_metadata=result.metadata,
             line=self.line,
-            md_headings=True,
         )
         _nodes = result.nb_renderer.render_markdown(mime)
         self.set_source_info(_nodes)

myst_nb/sphinx_.py

@@ -13,7 +13,8 @@
 from markdown_it.tree import SyntaxTreeNode
 from myst_parser.config.main import MdParserConfig, merge_file_level
 from myst_parser.mdit_to_docutils.base import token_line
-from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer, create_warning
+from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer
+from myst_parser.warnings_ import create_warning
 from myst_parser.parsers.mdit import create_md_parser
 from myst_parser.parsers.sphinx_ import MystParser
 import nbformat
@@ -262,7 +263,6 @@ def _render_nb_cell_code_outputs(
                 self.add_line_and_source_path_r(_nodes, token)
                 self.current_node.extend(_nodes)
             elif output.output_type in ("display_data", "execute_result"):
-
                 # Note, this is different to the docutils implementation,
                 # where we directly select a single output, based on the mime_priority.
                 # Here, we do not know the mime priority until we know the output format
@@ -504,9 +504,7 @@ class HideInputCells(SphinxPostTransform):
     formats = ("html",)
 
     def run(self, **kwargs):
-
         for node in findall(self.document)(nodes.container):
-
             if (
                 node.get("nb_element") == "cell_code"
                 and node.get("hide_mode")

pyproject.toml

@@ -39,7 +39,7 @@ dependencies = [
     "ipython",
     "jupyter-cache~=0.5.0",
     "nbclient",  # nbclient version pinned by jupyter-client
-    "myst-parser~=0.18.0",
+    "myst-parser~=1.0.0",
     "nbformat~=5.0",
     "pyyaml",
     "sphinx>=4,<6",
@@ -80,9 +80,9 @@ rtd = [
     "numpy",
     "pandas",
     "plotly",
-    "sphinx-book-theme~=0.3.0",
+    "sphinx-book-theme~=1.0.0",
     "sphinx-copybutton",
-    "sphinx-design~=0.1.0",
+    "sphinx-design~=0.3.0",
     "sphinxcontrib-bibtex",
     "sympy",
 ]

tests/nb_fixtures/reporter_warnings.txt

@@ -10,10 +10,9 @@ cells:
     source: |
         {unknown}`a`
 .
-<string>:20002: (ERROR/3) Unknown interpreted text role "unknown".
+<string>:20002: (WARNING/2) Unknown interpreted text role "unknown". [myst.role_unknown]
 .
 
-
 Unknown directive:
 .
 cells:
@@ -24,7 +23,7 @@ cells:
         ```{xyz}
         ```
 .
-<string>:10003: (ERROR/3) Unknown directive type "xyz".
+<string>:10003: (WARNING/2) Unknown directive type: 'xyz' [myst.directive_unknown]
 .
 
 Directive parsing error:
@@ -66,5 +65,5 @@ cells:
 
         [a]: c
 .
-<string>:20004: (WARNING/2) Duplicate reference definition: A [myst.ref]
-.
+<string>:20004: (WARNING/2) Duplicate reference definition: A [myst.duplicate_def]
+.